My first suggestion would be to double check your thermometer. Even if they have been accurate in the past they can go out. I had a thermometer that I had used successfully in the past. I just assumed it was right every time I used it and on the last incubation found that it was 3 degrees off 5 days into my incubation. Something seemed "off" and I checked it. Fortunately I did catch it but it did cost me half of my eggs. Now I "check" my thermometers before each use.
Second, I would look into running your bator just a touch higher. With still air you are aiming to get the core of your eggs at 99.5. To do this you want to have the TOP of your eggs at 101.5 (so in the range of 101-102) It does not sound like a lot of difference from what you are doing, but 1 degree CAN make a difference. Since you said that the yolk sacs where still exposed I would lean to under development due to low temps.
Now if you check your thermometer, and you change your temp, and you are still getting these issues then I would look into where you are getting your eggs from and consider a genetic issue. But I would start with the easiest to rule out first.
Good luck with your next hatch!